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Article ; Online: Many direct-to-consumer canine genetic tests can identify the breed of purebred dogs.

Rando, Halie M / Graim, Kiley / Hampikian, Greg / Greene, Casey S

Journal of the American Veterinary Medical Association

2024 Volume 262, Issue 5, Page(s) 1–8

Abstract: Objective: To compare pedigree documentation and genetic test results to evaluate whether user-provided photographs influence the breed ancestry predictions of direct-to-consumer (DTC) genetic tests for dogs.: Animals: 12 registered purebred pet dogs ...

Abstract	Objective: To compare pedigree documentation and genetic test results to evaluate whether user-provided photographs influence the breed ancestry predictions of direct-to-consumer (DTC) genetic tests for dogs. Animals: 12 registered purebred pet dogs representing 12 different breeds. Methods: Each dog owner submitted 6 buccal swabs, 1 to each of 6 DTC genetic testing companies. Experimenters registered each sample per manufacturer instructions. For half of the dogs, the registration included a photograph of the DNA donor. For the other half of the dogs, photographs were swapped between dogs. DNA analysis and breed ancestry prediction were conducted by each company. The effect of condition (ie, matching vs shuffled photograph) was evaluated for each company's breed predictions. As a positive control, a convolutional neural network was also used to predict breed based solely on the photograph. Results: Results from 5 of the 6 tests always included the dog's registered breed. One test and the convolutional neural network were unlikely to identify the registered breed and frequently returned results that were more similar to the photograph than the DNA. Additionally, differences in the predictions made across all tests underscored the challenge of identifying breed ancestry, even in purebred dogs. Clinical relevance: Veterinarians are likely to encounter patients who have conducted DTC genetic testing and may be asked to explain the results of genetic tests they did not order. This systematic comparison of commercially available tests provides context for interpreting results from consumer-grade DTC genetic testing kits.
Language	English
Publishing date	2024-02-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	390811-2
ISSN	1943-569X ; 0003-1488
ISSN (online)	1943-569X
ISSN	0003-1488
DOI	10.2460/javma.23.07.0372
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Dietary Supplements and Nutraceuticals under Investigation for COVID-19 Prevention and Treatment.

Lordan, Ronan / Rando, Halie M / Greene, Casey S

mSystems

2021 Volume 6, Issue 3

Abstract: Coronavirus disease 2019 (COVID-19) has caused global disruption and a significant loss of life. Existing treatments that can be repurposed as prophylactic and therapeutic agents may reduce the pandemic's devastation. Emerging evidence of potential ... ...

Abstract	Coronavirus disease 2019 (COVID-19) has caused global disruption and a significant loss of life. Existing treatments that can be repurposed as prophylactic and therapeutic agents may reduce the pandemic's devastation. Emerging evidence of potential applications in other therapeutic contexts has led to the investigation of dietary supplements and nutraceuticals for COVID-19. Such products include vitamin C, vitamin D, omega 3 polyunsaturated fatty acids, probiotics, and zinc, all of which are currently under clinical investigation. In this review, we critically appraise the evidence surrounding dietary supplements and nutraceuticals for the prophylaxis and treatment of COVID-19. Overall, further study is required before evidence-based recommendations can be formulated, but nutritional status plays a significant role in patient outcomes, and these products may help alleviate deficiencies. For example, evidence indicates that vitamin D deficiency may be associated with a greater incidence of infection and severity of COVID-19, suggesting that vitamin D supplementation may hold prophylactic or therapeutic value. A growing number of scientific organizations are now considering recommending vitamin D supplementation to those at high risk of COVID-19. Because research in vitamin D and other nutraceuticals and supplements is preliminary, here we evaluate the extent to which these nutraceutical and dietary supplements hold potential in the COVID-19 crisis.
Language	English
Publishing date	2021-05-04
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2379-5077
ISSN	2379-5077
DOI	10.1128/mSystems.00122-21
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Dietary Supplements and Nutraceuticals Under Investigation for COVID-19 Prevention and Treatment.

Lordan, Ronan / Rando, Halie M / Greene, Casey S

ArXiv

2021

Abstract: Coronavirus disease 2019 (COVID-19) has caused global disruption and a significant loss of life. Existing treatments that can be repurposed as prophylactic and therapeutic agents could reduce the pandemic's devastation. Emerging evidence of potential ... ...

Abstract	Coronavirus disease 2019 (COVID-19) has caused global disruption and a significant loss of life. Existing treatments that can be repurposed as prophylactic and therapeutic agents could reduce the pandemic's devastation. Emerging evidence of potential applications in other therapeutic contexts has led to the investigation of dietary supplements and nutraceuticals for COVID-19. Such products include vitamin C, vitamin D, omega 3 polyunsaturated fatty acids, probiotics, and zinc, all of which are currently under clinical investigation. In this review, we critically appraise the evidence surrounding dietary supplements and nutraceuticals for the prophylaxis and treatment of COVID-19. Overall, further study is required before evidence-based recommendations can be formulated, but nutritional status plays a significant role in patient outcomes, and these products could help alleviate deficiencies. For example, evidence indicates that vitamin D deficiency may be associated with greater incidence of infection and severity of COVID-19, suggesting that vitamin D supplementation may hold prophylactic or therapeutic value. A growing number of scientific organizations are now considering recommending vitamin D supplementation to those at high risk of COVID-19. Because research in vitamin D and other nutraceuticals and supplements is preliminary, here we evaluate the extent to which these nutraceutical and dietary supplements hold potential in the COVID-19 crisis.
Language	English
Publishing date	2021-02-03
Publishing country	United States
Document type	Preprint
ISSN	2331-8422
ISSN (online)	2331-8422
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Coming of Age of Nucleic Acid Vaccines during COVID-19.

Rando, Halie M / Lordan, Ronan / Kolla, Likhitha / Sell, Elizabeth / Lee, Alexandra J / Wellhausen, Nils / Naik, Amruta / Kamil, Jeremy P

ArXiv

2023

Abstract: In the 21st century, several emergent viruses have posed a global threat. Each pathogen has emphasized the value of rapid and scalable vaccine development programs. The ongoing SARS-CoV-2 pandemic has made the importance of such efforts especially clear. ...

Abstract	In the 21st century, several emergent viruses have posed a global threat. Each pathogen has emphasized the value of rapid and scalable vaccine development programs. The ongoing SARS-CoV-2 pandemic has made the importance of such efforts especially clear. New biotechnological advances in vaccinology allow for recent advances that provide only the nucleic acid building blocks of an antigen, eliminating many safety concerns. During the COVID-19 pandemic, these DNA and RNA vaccines have facilitated the development and deployment of vaccines at an unprecedented pace. This success was attributable at least in part to broader shifts in scientific research relative to prior epidemics; the genome of SARS-CoV-2 was available as early as January 2020, facilitating global efforts in the development of DNA and RNA vaccines within two weeks of the international community becoming aware of the new viral threat. Additionally, these technologies that were previously only theoretical are not only safe but also highly efficacious. Although historically a slow process, the rapid development of vaccines during the COVID-19 crisis reveals a major shift in vaccine technologies. Here, we provide historical context for the emergence of these paradigm-shifting vaccines. We describe several DNA and RNA vaccines and in terms of their efficacy, safety, and approval status. We also discuss patterns in worldwide distribution. The advances made since early 2020 provide an exceptional illustration of how rapidly vaccine development technology has advanced in the last two decades in particular and suggest a new era in vaccines against emerging pathogens.
Language	English
Publishing date	2023-01-24
Publishing country	United States
Document type	Preprint
ISSN	2331-8422
ISSN (online)	2331-8422
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Application of Traditional Vaccine Development Strategies to SARS-CoV-2.

Rando, Halie M / Lordan, Ronan / Lee, Alexandra J / Naik, Amruta / Wellhausen, Nils / Sell, Elizabeth / Kolla, Likhitha / Gitter, Anthony / Greene, Casey S

ArXiv

2023

Abstract: Over the past 150 years, vaccines have revolutionized the relationship between people and disease. During the COVID-19 pandemic, technologies such as mRNA vaccines have received attention due to their novelty and successes. However, more traditional ... ...

Abstract	Over the past 150 years, vaccines have revolutionized the relationship between people and disease. During the COVID-19 pandemic, technologies such as mRNA vaccines have received attention due to their novelty and successes. However, more traditional vaccine development platforms have also yielded important tools in the worldwide fight against the SARS-CoV-2 virus. A variety of approaches have been used to develop COVID-19 vaccines that are now authorized for use in countries around the world. In this review, we highlight strategies that focus on the viral capsid and outwards, rather than on the nucleic acids inside. These approaches fall into two broad categories: whole-virus vaccines and subunit vaccines. Whole-virus vaccines use the virus itself, either in an inactivated or attenuated state. Subunit vaccines contain instead an isolated, immunogenic component of the virus. Here, we highlight vaccine candidates that apply these approaches against SARS-CoV-2 in different ways. In a companion manuscript, we review the more recent and novel development of nucleic-acid based vaccine technologies. We further consider the role that these COVID-19 vaccine development programs have played in prophylaxis at the global scale. Well-established vaccine technologies have proved especially important to making vaccines accessible in low- and middle-income countries. Vaccine development programs that use established platforms have been undertaken in a much wider range of countries than those using nucleic-acid-based technologies, which have been led by wealthy Western countries. Therefore, these vaccine platforms, though less novel from a biotechnological standpoint, have proven to be extremely important to the management of SARS-CoV-2.
Language	English
Publishing date	2023-01-23
Publishing country	United States
Document type	Preprint
ISSN	2331-8422
ISSN (online)	2331-8422
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Application of Traditional Vaccine Development Strategies to SARS-CoV-2.

Rando, Halie M / Lordan, Ronan / Lee, Alexandra J / Naik, Amruta / Wellhausen, Nils / Sell, Elizabeth / Kolla, Likhitha / Gitter, Anthony / Greene, Casey S

mSystems

2023 Volume 8, Issue 2, Page(s) e0092722

Abstract: ... ways. In a companion article (H. M. Rando, R. Lordan, L. Kolla, E. Sell, et al., mSystems 8:e00928-22 ...

Abstract	Over the past 150 years, vaccines have revolutionized the relationship between people and disease. During the COVID-19 pandemic, technologies such as mRNA vaccines have received attention due to their novelty and successes. However, more traditional vaccine development platforms have also yielded important tools in the worldwide fight against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A variety of approaches have been used to develop COVID-19 vaccines that are now authorized for use in countries around the world. In this review, we highlight strategies that focus on the viral capsid and outwards, rather than on the nucleic acids inside. These approaches fall into two broad categories: whole-virus vaccines and subunit vaccines. Whole-virus vaccines use the virus itself, in either an inactivated or an attenuated state. Subunit vaccines contain instead an isolated, immunogenic component of the virus. Here, we highlight vaccine candidates that apply these approaches against SARS-CoV-2 in different ways. In a companion article (H. M. Rando, R. Lordan, L. Kolla, E. Sell, et al., mSystems 8:e00928-22, 2023, https://doi.org/10.1128/mSystems.00928-22), we review the more recent and novel development of nucleic acid-based vaccine technologies. We further consider the role that these COVID-19 vaccine development programs have played in prophylaxis at the global scale. Well-established vaccine technologies have proved especially important to making vaccines accessible in low- and middle-income countries. Vaccine development programs that use established platforms have been undertaken in a much wider range of countries than those using nucleic acid-based technologies, which have been led by wealthy Western countries. Therefore, these vaccine platforms, though less novel from a biotechnological standpoint, have proven to be extremely important to the management of SARS-CoV-2.
MeSH term(s)	Humans ; SARS-CoV-2 ; COVID-19/prevention & control ; COVID-19 Vaccines ; Pandemics/prevention & control ; Viral Vaccines ; Vaccine Development ; Vaccines, Subunit ; Nucleic Acid-Based Vaccines
Chemical Substances	COVID-19 Vaccines ; Viral Vaccines ; Vaccines, Subunit ; Nucleic Acid-Based Vaccines
Language	English
Publishing date	2023-03-02
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ISSN	2379-5077
ISSN (online)	2379-5077
DOI	10.1128/msystems.00927-22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography.

Sacks, Benjamin N / Lounsberry, Zachary T / Rando, Halie M / Kluepfel, Kristopher / Fain, Steven R / Brown, Sarah K / Kukekova, Anna V

Genes

2021 Volume 12, Issue 1

Abstract: The red fox ( ...

Abstract	The red fox (
MeSH term(s)	Animals ; Foxes/genetics ; Male ; Phylogeography ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Y Chromosome/genetics
Language	English
Publishing date	2021-01-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12010097
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Coming of Age of Nucleic Acid Vaccines during COVID-19.

Rando, Halie M / Lordan, Ronan / Kolla, Likhitha / Sell, Elizabeth / Lee, Alexandra J / Wellhausen, Nils / Naik, Amruta / Kamil, Jeremy P / Gitter, Anthony / Greene, Casey S

mSystems

2023 Volume 8, Issue 2, Page(s) e0092822

Abstract: In the 21st century, several emergent viruses have posed a global threat. Each pathogen has emphasized the value of rapid and scalable vaccine development programs. The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has ... ...

Abstract	In the 21st century, several emergent viruses have posed a global threat. Each pathogen has emphasized the value of rapid and scalable vaccine development programs. The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has made the importance of such efforts especially clear. New biotechnological advances in vaccinology allow for recent advances that provide only the nucleic acid building blocks of an antigen, eliminating many safety concerns. During the COVID-19 pandemic, these DNA and RNA vaccines have facilitated the development and deployment of vaccines at an unprecedented pace. This success was attributable at least in part to broader shifts in scientific research relative to prior epidemics: the genome of SARS-CoV-2 was available as early as January 2020, facilitating global efforts in the development of DNA and RNA vaccines within 2 weeks of the international community becoming aware of the new viral threat. Additionally, these technologies that were previously only theoretical are not only safe but also highly efficacious. Although historically a slow process, the rapid development of vaccines during the COVID-19 crisis reveals a major shift in vaccine technologies. Here, we provide historical context for the emergence of these paradigm-shifting vaccines. We describe several DNA and RNA vaccines in terms of their efficacy, safety, and approval status. We also discuss patterns in worldwide distribution. The advances made since early 2020 provide an exceptional illustration of how rapidly vaccine development technology has advanced in the last 2 decades in particular and suggest a new era in vaccines against emerging pathogens.
MeSH term(s)	Humans ; COVID-19/epidemiology ; SARS-CoV-2/genetics ; COVID-19 Vaccines ; Nucleic Acid-Based Vaccines ; Pandemics/prevention & control ; Viral Vaccines ; mRNA Vaccines
Chemical Substances	COVID-19 Vaccines ; Nucleic Acid-Based Vaccines ; Viral Vaccines ; mRNA Vaccines
Language	English
Publishing date	2023-03-02
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2379-5077
ISSN (online)	2379-5077
DOI	10.1128/msystems.00928-22
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: An Open-Publishing Response to the COVID-19 Infodemic.

Rando, Halie M / Boca, Simina M / McGowan, Lucy D'Agostino / Himmelstein, Daniel S / Robson, Michael P / Rubinetti, Vincent / Velazquez, Ryan / Greene, Casey S / Gitter, Anthony

CEUR workshop proceedings

2022 Volume 2976, Page(s) 29–38

Abstract: The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis ... ...

Abstract	The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures present unique challenges to collaborative science. We applied a massive online open publishing approach to this problem using Manubot. Through GitHub, collaborators summarized and critiqued COVID-19 literature, creating a review manuscript. Manubot automatically compiled citation information for referenced preprints, journal publications, websites, and clinical trials. Continuous integration workflows retrieved up-to-date data from online sources nightly, regenerating some of the manuscript's figures and statistics. Manubot rendered the manuscript into PDF, HTML, LaTeX, and DOCX outputs, immediately updating the version available online upon the integration of new content. Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1,500 sources and developed seven literature reviews. While many efforts from the computational community have focused on mining COVID-19 literature, our project illustrates the power of open publishing to organize both technical and non-technical scientists to aggregate and disseminate information in response to an evolving crisis.
Language	English
Publishing date	2022-03-14
Publishing country	Germany
Document type	Journal Article
ISSN	1613-0073
ISSN	1613-0073
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Molecular and Serologic Diagnostic Technologies for SARS-CoV-2.

Rando, Halie M / Brueffer, Christian / Lordan, Ronan / Dattoli, Anna Ada / Manheim, David / Meyer, Jesse G / Mundo, Ariel I / Perrin, Dimitri / Mai, David / Wellhausen, Nils / Gitter, Anthony / Greene, Casey S

ArXiv

2022

Abstract: The COVID-19 pandemic has presented many challenges that have spurred biotechnological research to address specific problems. Diagnostics is one area where biotechnology has been critical. Diagnostic tests play a vital role in managing a viral threat by ... ...

Abstract	The COVID-19 pandemic has presented many challenges that have spurred biotechnological research to address specific problems. Diagnostics is one area where biotechnology has been critical. Diagnostic tests play a vital role in managing a viral threat by facilitating the detection of infected and/or recovered individuals. From the perspective of what information is provided, these tests fall into two major categories, molecular and serological. Molecular diagnostic techniques assay whether a virus is present in a biological sample, thus making it possible to identify individuals who are currently infected. Additionally, when the immune system is exposed to a virus, it responds by producing antibodies specific to the virus. Serological tests make it possible to identify individuals who have mounted an immune response to a virus of interest and therefore facilitate the identification of individuals who have previously encountered the virus. These two categories of tests provide different perspectives valuable to understanding the spread of SARS-CoV-2. Within these categories, different biotechnological approaches offer specific advantages and disadvantages. Here we review the categories of tests developed for the detection of the SARS-CoV-2 virus or antibodies against SARS-CoV-2 and discuss the role of diagnostics in the COVID-19 pandemic.
Language	English
Publishing date	2022-04-26
Publishing country	United States
Document type	Preprint
ISSN	2331-8422
ISSN (online)	2331-8422
Database	MEDical Literature Analysis and Retrieval System OnLINE

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